Star Trek: Lyoko
by AStarShifter
Summary: A Star Trek/Code Lyoko Story Set in the year 2943, with Aelita and the Gang Fighting XANA, With the Help of The Crew of The USS Flux NGV-28403 E, and Section 23
1. Chapter 1

Chapter 1 XANA Re-Awakens

The Year 2004

Good by XANA says a young blond boy He then pulls a switch on a cylindrical machine covered with gold sparkling light. The light goes out and lowers into the floor and a hatch with a kind of eye closes on top of it

The Present (2943)

Alaya Is Regenerating in her alcove, her eyes open and the computer can be herd saying Regeneration cycle Complete The young, blue haired girl, in her night clothes, a blue oversized shirt with a large Starfleet insignia (2371), and blue short shorts. After changing into her uniform and consuming her breakfast, Alaya went to engineering.  
I am going to Engineering to assist Lt. Gates, and Crewman Ether repair the sensor arrays, I have estimate that it will take 67 minuets, including 27 minuets for Jim Gates, and Jason Ether s attempts at conversation

2942 (Five Months Prior, aboard the San Francisco)  
On a mission to research some strange readings, in a surprising location Boulogne-Billancourt, France. There In an old abandoned factory, we discovered 3 Lower stories then what was on the schematics, On top of that We Found advanced technology, which after quantum dating was reveled to be almost 1,000 years old. A Massive computer we then Copied Every Bit of Data Form it, and found what appeared to be a map of the Earth with Other computers marked on it, Not due at space dock for a few more days we went to the locations, and Found that of the 360 computers marked 120 of them survived. These other computers were not as advanced but we proceeded to use Other Data Cores to Download All the Data in them. Captains Log

In some Jeffries tube 45 minuets later So as a Drone you weren t with any guys were you? Jason Are you referring to mating? Alaya said coldly No! NO! I meant out on a date? A first kiss? A First Love? No, Borg do not feel love . Alaya However the Borg Have referenced romantic love in over 19,000 assimilated species Alaya 20 minuets, and many questions later This Task is complete Alaya Alaya Would you like to come to the mess hall with us? Jason No Alaya What about going to the Holode Jim, as Alaya cuts him off No

2943 (3 Months Prior, aboard the San Francisco)  
Captains log. We were hit by a massive ion Storm, and it damaged some systems. Many of the crew have gone missing, with no explanation

Later That day (Present)  
The Captain has encouraged me to visit the Mess hall more Often, but I feel, I feel Strange in the more populated areas of the ship. Some the male crew members keep making advances toward me, I believe it is an attempt to mate, Humans are very Unique . Alaya Personal Log, 4-23-2943 Alaya her comm. badge beeps She taps it, Yes Captain Come to the Bridge, we need you expertise Axum Affirmative Alaya says as she walks down the hall to a turbo lift Bridge Alaya commands the compute A minuet later Alaya arrives On the Bridge Captain Axum, Captain Torrie Alaya says Alaya, did you request we go to Memory Galactica? Torrie Yes. Why? Torrie Because Starfleet wants us to locate the USS San Francisco, which went missing in the vicinity of Memory Galactica, and Starfleet is willing to allow you to visit. If you Help Retrieve the San Francisco Axum I will comply. Alaya

2943 (2 Months Prior, aboard the San Francisco)  
We are locked out of all systems, and some kind of Eye has appeared on all the monitors, and we only have 13 crewmen left

Present Day (The Mess Hall)  
Alaya is working on a PADD at a table, William is sitting with her also working on a PADD Hey Will!! Tony William dose not look up but gets an irritated look on his face Just then the Ships 21 year old Pilot, Tony Sits at the table with them, with a tray of food. Between chewing he manages to get out I never thought that you and her would ever sit at the same table. I mean don t you hate each other, you re a Groundskeeper and she s a Borg?  
Tony, no offense but we would prefer you to be quiet William None taken Tony says disappointed 5 minuets later What you working on Alaya? Tony I believe what are you working on. And I am working on a way to improve the ships Slip stream periscopes, as well as Reading about aspects of humanity Alaya Interesting, what aspects of humanity are you reading up on? Tony asks showing some interest

2943 (1 Month Prior, aboard the San Francisco)  
Acting Captains log, we have determined that a virus has infected the ships main computer, but we could not get rid of. Now I am the only member of the crew left on the ship. All attempts to alert Starfleet have failed. This will likely be the last log form the USS San Francisco, NGV-374122

The Present The Human concept of romantic Love. Alaya You should research there Complex Mating Rituals William I am amazed the human race still exists using this form of Maiting

2943 (1 week Prior, aboard the San Francisco)  
Acting Captains Log, The Virus is deleting the Logs, I have encrypted all the logs I can. The Virus Has Identified It s self as Xan 


	2. Chapter 2

Chapter 2 The San Francisco

After the Flux arrives at the powerless San Francisco Report to the Transporter room Alaya s Comm. Badge Beeped On my way Alaya In the transporter room This is the away team, Lt. Gates, Lt. Jones, Doctor MaKie, Ensign Jenkins, and Alaya Rhodes Axum Prepare for Transport Energize

After the Crew reapers aboard the Dark San Francisco The Lights are out Tony Keen observation Jenkins William Doctor MaKie, You and me will try to find out where the crew is Rori Jones I will go to the bridge and try to turn the power back on Gates Alaya, Tony go to engineering Rori

In Engineering I found something Tony I did as well Alaya Alaya taps her badge Jones, Gates. I found how to reactivate the ship How? Rori We Must re-link all the systems back together Alaya That would take Months Gates Incorrect, the Ship s circuitry is Organic, so if I modify some of my nanoprobes to infect, then repair the circuitry is should just take 3 or 4 hours Alaya Begin Immediately Rori After she starts, Alaya looks around the ship. In the Science lab she finds A strange Memory Core, it has a Gold Eye like thing engraved on the top. It appears Damaged. Alaya Maybe I should try and salvage this, Torrie said I could take any thing I wanted unless it was in someone s quarters She then picks the Core up and puts it away in her bag, and continues to look around the ship for spare parts Suddenly the ship Shakes Sorry, But we Locked a tractor beam on to the Ship, It s time to beam over says Axum thru Alaya s Comm badge Alaya quickly walks back to the transport site

3 hours later Primary power online. The Nanoprobes worked. Alaya First thing we need to do is to get this ship back to Memory Galactica Axum Alaya can be seen looking slightly excited (For her that s extremely excited)  
Alaya Axum Yes. Alaya You will be accompanied by Doctor MaKie, Lt. Ether, Ensign Jenkins, Lt. Gates, and I Axum I believe the human expression is Thank you . Alaya Your Welcome Alaya, the others will show you the guest quarters when we arrive Outside the window the stars change from points into streaks of light the ship was At warp.  
We are at warp 5, we will arrive at Memory Galactica in 10 hours 6 hours later in Alaya s Science Lab, Alaya has set out the Strange Memory core on the analyzing table and is in her alcove Regenerating.  
The memory core begins lighting up and sends electricity out of itself and then goes off again, on the Table s console a White Eye, the same symbol as on the top of the Core appears on screen then begins accessing programs. The Lights in the Lab begin Turning on and off and screens begin to flicker. Then things begin to appear in Borg charters, the theme then changes tcars to a Borg-tcars hybrid and the problem stops, the lights turn off, but the white Symbol is still on one screen. Alaya s eyes Open, and the computer warns Warning Regeneration cycle incomplete Computer, Begin Interface with Data Core E112. Authorization Rhodes Omega 4 7 9. Begin accessing all usable data Alaya Can not comply. Data is Incompatible with tcars computer system. Computer Computer Begin working on altering an interface port compatible Alaya Affirmative Estimate time to completion Alaya 45 minuets Computer Alaya turns and notices the Symbol What is this The Symbol then opens up a window; on it is written Welcome to Carthage it also has a spot for a password Computer what is this symbol? Alaya Unknown Computer Computer, what is Carthage? Alaya Carthage: Carthage, an ancient city-state in North Africa, Earth, Carthage, Ontario, Carthaginian Empire, informal empire Alaya interrupts Send all information on Carthage Option 1 to my alcove room Alaya Affirmative After she read the information, Alaya began to try and figure out the password Computer, can you tell me what is in the password? Alaya S, C, I Computer Cross reference Carthage Alaya Scipio Africanus Computer Alaya types in SCIPIOAFRICANUS enter Access Denied She types SCIPIO Access Approved The Display opens up a window on the display it shows a 3D diagram of a Sphere with four spokes coming out of it and zooms it into the center and shows 4 green triangles with one yellow one, five cards pop up and Have images of Five Kids in strange clothing. It pops up a window with program codes on it and begins to scroll down After a few minuets, Alaya transfers the display to her PADD Doctor MaKie, Please Meet me in the Mess hall Alaya Why? William I found something strange aboard the San Francisco Alaya Ok William In the Mess Hall I found a Data Core with incompatible programs, but I managed to open afew they are very strange. Alaya How William They are form Earth s Early 21st century, but these programs are immensely complex, they are comparable to some late 26th century programs, they also contain bits and pieces of Transporter codes, and parts of a temporal incursion program. Your data is flawed, humanity didn t have any transporter technology until the 22nd century, and no computer of that time would be able to hold that amount of data William I rechecked the data and it seems likely that it is 97% correct Alaya I know someone who might Know, He excels at old Earth history, and is good at transporter physics, and is kind of good at computer codes William Who? Alaya asked Ensign Ton... William is interrupted by Alaya with a Firm No. Alaya, Captain Paris told me to help you fit in with humans, this is a good opportunity to just that William No. Alaya Why? William I find him Annoying, and I think he is Overactive Alaya says quieting down to a whisper Many Humans Are Annoying. Ask Him for Help. If you prefer, I will accompany you during this Investigation , I believe I can also be of some use to you any way William Fine. Meet me in my lab in 10 minuets Alaya

10 minuets later, in Alaya s lab Hello Alaya, Where is Tony? William said with a disappointed look on his face I have not contacted him yet. I was about to, but you interrupted me Alaya Computer Contact Tony Jenkins In Tony s Quarters.  
The room is dark clothes are on the floor, and someone s in the bed (-). BEEP. BEEP.  
Tony Tony, Would you Please Come to My Lab. Immediately Alaya s voice can be heard Some one gets up out of the bed, It s Tony, and he s warring only boxers (very typical). He stars getting dressed. There s someone else in the bed.  
Go back to Sleep Amy Tony says softly (OMG!!)

5 Minuets later in Alaya s Lab. Swoosh Door slides open and closed Tony, Welcome. I need some of your help. Alaya Alaya I was in the middle of something important , what do you need Tony, I need you to check over this data. And Determine if these transporter codes work Alaya s instructs Tony as she hands him several PADDs Alaya, what is this for? Tony asks At this point I do not know Alaya States Alaya, some of these things are written in Borg Alphanumeric code Tony Yes what is the problem Alaya I, like most people can t read Borg! Tony says Irritated Oh I am, how you say Sorry Alaya says as she presses a few buttons and everything on screens transfers into a tcars Mode

3 Hours Later We Have Arrived at Memory Galactica, Prepare to dock 


	3. Chapter 3

Chapter 3 What Happens in Memory Galactica Stays There

We Have Arrived at Memory Galactica, Prepare to dock. Shut down tractor beam.  
Away team, Gather your stuff it s Time to go Axum

A few minuets later in the Hotel Section of Memory Galactica.  
I was only able to secure 2 rooms, and there are six of us so let s work out who bunks with who. Axum I will take Rhodes, and Jenkins William I guess that means that Me, The Captain, and Jason are together Jim MaKie you re in room 5673, Jason we re in room 5889 Axum

Later in MaKie s room This must not be the right room, there are only 2 beds William That means two of us need to share a bed Tony says as he slides up to Alaya Incorrect assumption Tony, I will require a minimum of sleep on this Assignment Alaya Perfect Tony says hiding disappointment I Call first use of the Bathroom Alaya Says 10 minuets later Alaya comes out in her night clothes Finally some of us needed to use the Bathroom for more important reasons Tony says as he runs in to the Bathroom He said to have drunk a lot of something Called Soda , it smelled horrible to me William Typical Alaya Would you turn away please, I need to change clothes William Alaya turns away Why did you Chose Me? I felt that you would be more comfortable with me William Your assumption was based on what? Alaya You seem to be a kindred spirit, you and I do not fit in with other People. William tells her Your Assumption Was Correct Alaya But why did you pick Tony?! It seems strange but It seems like he is helping you ease into humanity William No he s not Alaya He is annoying, I know but he helps you deal with humans better. You are kinder to him then you are to other people No I am not! Alaya A few days ago, in the mess hall, those two crewmen came up to you and asked if you wanted to come visit the Holodeck, you cut them off before the finished asking Alaya That proves nothing Alaya The Next day Tony asked you the same thing, you asked what he had in mind. He said Volleyball, You said I have to decline, maybe some other time William But am I am nice to you Alaya Asserts I also am the one who removed most of you Borg Implants I do not wish to continue this Conversation Then the Bathroom door opens and closes, to revel Tony Tony, you took of you uniform William (he is in a tank top and Boxers (Star Fleet brand Boxers, There Shields are Never Down )  
This Is Shore leave, and I don t want to be stuck in that uniform all the time. Besides It s Not Like I m going to walk around like this Tony, there are Other People in here William Mumbles as he gestures to Alaya Oh, sorry Tony says as he Tucks in his shirt That night at 0100 hours (1 in the morning) Tony is making strange moaning noises in his bed. William is holding the Pillows to his Ears, and Alaya is sleeping on the couch with her PADD which is still running with thru Data. Suddenly the PADD displays that White Eye symbol, and begins running programs and Comes up with a window that shows those 5 green and yellow triangles. One of the Cards this one with the girl with Pink Hair pops with a strange window Jeremie a voice says Jeremie other voices shout, this wakes Alaya up Who s there Alaya says in a uneasy voice You re not Jeremie. Where s Jeremie? the first voice says Alaya realizing the voices are coming from her PADD, She picks It Up and Asks/Demands State Your Designation Who are you? What s happened with Jeremie? I am Alaya Rhodes Alaya Says Now State Your Designation!! I am Aelita Stones, How Did you get into the factory? Aelita asks What factory? Alaya Asks The Old Abandoned factory near Kadic! Another Voice Shouts William, Ulrich, Calm down Aelita tells the other voices We are at Memory Galactica Alaya Responds Memory what-aca? Ulrich Says Memory Galactica, A Memory Planet Alaya Impossible Some other male voice states We are In France, Boulogne-Billancourt France France? Earth s France? YES!!! How many other Frances are there!?! Ulrich Yells Earth is 1,239.5 Light years away. What Time period are you from? Alaya Demands 2004, what are you crazy Aelita 2004 was 939 years ago, the year is 2943 Alaya Impossible, you are CRAZY they shout I can Prove it, I am opening The Video and Audio sensors, and in one second Alaya says as she Entered codes And You Should Have the Image In Some Strange Blue Domed Room Stands Five Kids in strange cloths, All in Form fitting Body suits, One Guy had Very Strange pointy blond Hair (Odd) and Cat Ears In this strange Place a screen appears floating in mid air, on it is Alaya s Face I would Like to return the Favor Aelita Says as She Sends Alaya a Visual My evidence Alaya Says as she holds up her hand Is This The Group of kids see her hand Covered with a silver web like thing It s Part of my remaining Artificial Exo-skeleton Your Not Human Are you? William (Referred to from now on as Will) Asks I am, but this is Borg Who are the Borg? Aelita Asks I would Rather not Talk about it at this time Alaya Can You Materialize Us? Odd Asks I do not know what you mean? Wait dose that involve the transporter program? Alaya It Might. But what is a transporter? Aelita Asks Give me a Day or two and I can Materialize you Alaya says as she cuts the line

The Next Day at 2300 (11pm)  
Tony is sleeping on the couch once again is making strange noises, Alaya is sleeping in her bed (She s Borg and Tones out Tony, that and the doctor gave her a sedative to help her sleep. William is sleeping with headphones on. Alaya is tossing and turning

In Alaya s Dream (Oww Ohh Oww)  
3 of 12 auxiliary processor of Trimatrix 09, Your Wishes are Irrelevant. You will be assimilated. Resistance is futile the Voice of the Borg Nooo Alaya s mom screams Alaya Run, Hide!!! Her Dad Screams A young Alaya (3 years old) is running thru the halls of a Star Ship Screaming, a Borg Drone Steps Out of a Door You are Week. You Are Irrelevant. You are nothing with out us Alaya Screams and Continues running now at her current age (around 20)  
Suddenly dozens of drones are following her. She makes it to the shuttle bay. Just as she enters thru the Door Two drones grab her and She Hears We Are the Borg. Existence as you know it is over. You will be assimilated. Resistance is futile Alaya Screams as the drone plunges the assimilation tubules into her neck She Wakes Up Scared and thinks William is trying to sleep, And Tony is the only one around. Tony not actually sleeping Sits up, and Asks Alaya Alaya what s wrong N Nothings wrong Alaya says stuttering, and obviously upset (Warning Special Moment About to Happen (Nothing Inappropriate)  
Tony gets up walks over to Alaya s bed, and sits next to Alaya Alaya are you all right? Tony asks gently It is my parents, I don t really know, I have been having terrible dreams Alaya says Alaya there only dreams Tony says trying to reassure her I Hear them Alaya Who? Your parents Tony asks No, the Collective Alaya Alaya, they can t hurt you. You re safe here Alaya starts crying, Tony puts his arm around her, and she starts crying into his shoulder Don t worry They Can t hurt you I won t let them Tony says After a few minuets Alaya and Tony Fall asleep, Alaya still on Tony s shoulder (FYI She is under the blanket, he s on top of the blanket)

In the Morning William Grabs Tony shirt by his arm and drags him away from the bed What Did You Do!?! William Demands What? Nothing! I would Never! Why would you think something like that?! Tony Almost shouts Because, I know you like her, and given your History with women, it is a Very logical Conclusion William And She was sleeping on your shoulder, and your arm was around her! Tell me the truth! Did you Do Anything!?! We didn t do anything!!! Tony And you won t Do Anything, Not with her!!! William Shouts I won t!! Tony Shouts Don t Worry. Let me Go!! Tony squirms At that point Alaya wakes up What are you doing? Alaya Asks At that point William Drops Tony, and they both act as if nothing is wrong Nothing They Both Say in unison I am going to change Alaya says as she walks into the bathroom Oh!! Alaya Today We Leave At 1600 (4pm) William Says Tony Get Back into your uniform William Orders But Alaya s using the Bathroom Tony says confused I Said Now William But Tony William thinking back to his academy days and remembers something What. Are you embarrassed we are both Male William Says If you would like I ll turn around. I Am the Flux doctor, so I get how some men are Embarrassed William says out of Character What! Are you talking about tony Says Blushing And You Can t Talk How Do We know what gender you are! My spices has 5 genders, Including the traditional Male, and Female, I am Male After they change into there uniforms. Swoosh the bathroom door opens Hello Alaya Tony William, you I need five mobile emitters, and Help transferring some of the strange programs regarding Lyoko into holograms Alaya Ok. But I can t promise 5 mobile emitters Tony says As he leaves Doctor, I need you to age 5 people by 6 years by the time we leave Alaya Ok, I ll try, just give me there specifications William. Alaya hands him a PADD.

On the Shuttle Headed for where the flux is docked (Like a monorail but on the outside of the base)  
Tony, did you get the emitters? Alaya asked Yes, I got all five Tony Thank you. When we get back to the ship, I will reserve Some Holodeck time, I expect you both to be there Alaya William and Tony look shocked at her Really! Tony says excited 


	4. Chapter 4

Chapter 4 Welcome to Lyoko

On Lyoko Ulrich, Will, and Yumi are training together, and Aelita and Odd are exploring Sector 5 Suddenly a series of small white tremors travel throughout the corridors of Carthage Aelita and Odd seem to be having fun. Aelita senses the tremors and Whispers Pulsations What? Odd Asks Pulsations! Aelita Says worried What? Are you sure?! Odd asks seeming very worried XANA Odd asks I m not sure, but I think so Aelita What do you think we should do? Odd Go Warn the others, I ll go and find the source of the Pulsations Aelita Let s meet up in the Arena Odd

The Flux s Holodeck Alaya is on the Holodeck in a beautiful Blue dress, holding her PADD, and with a bag full of the Strange Data Cores Computer Time Alaya demands 16:14(4:14) the computer responds Then the door opens Tony walks in, dressed in a black T-shirt, and orange pants.  
Welcome Tony Alaya Hi Alaya Tony says blushing Sorry. I did not know what to wear. I thought this might be appropriate Alaya says obviously Embarrassed.  
William walks into the room, dressed in a gray tank top, and Star fleet blue jeans Welcome, now that we are all here, we can begin Alaya Computer Open Interface port Alaya demands as she walks over to the control arch, she places the Data core with the strange Eye (The one that contains Lyoko) on the now reveled interface port. And begins activating programs I hear that this can tingle when you first undergo the procedure Alaya What are you doing? Tony asks At that moment Alaya walks out into the room and says Begin Then three bright columns of light appear over the group Alaya, I can t move Tony Do not worry Alaya says calmly Two circles of light form around the group, and begin moving vertically over them, seeming to scan them. After a few seconds of that a burst of light.

On Lyoko Odd, Yumi, Will, and Ulrich arrive in the arena, and to there surprise they find 3 strange people on the floor Who are they? Odd I think there unconscious Yumi Alaya starts to wake Look out!! Ulrich Yells, The group gets ready to attack. Alaya stands up Alaya? Alaya is that you? Odd Asks Yes. You are Odd I presume? Alaya It s ok this is Alaya Odd reassures everyone It s Nice to Meet You Yumi begins to say but Alaya Cuts her Off Where Is Aelita? Aelita is Not here at this moment Odd Yumi whispers to Will Not very nice is she I must Wake William, and Tony Alaya says as she kneels down to William. Alaya makes a fist and two tubes come out of her hand and stick into William s neck, William winces in pain, but wakes up Alaya Never do that again, where are we? William asks as he rubs where Alaya stuck two tubes into him We are in a Holographic Projection of A Program in the Data Core Alaya Says as she moves to do the same thing to Tony Alaya Who are these kids? William Asks These are those programs I need you to alter Alter? What do you mean? Ulrich Asks Your programs are degraded, you will not exist much longer unless you are repaired Alaya Alaya who are these people? Odd asks as Aelita Walks in These are my crewmates, Doctor William MaKie, and Ensign Tony Jenkins Alaya explains Aelita Asks Odd Who are these People? Odd informs her This is Alaya and her friends Aelita. Can you take me to a Computer Interface? Alaya asks Um Sure, I ll take you to the tower. But first I need to talk to my friends, privately Aelita As the Lyoko Worriers gather into a circle I don t think it s XANA, I could not find any trace of an attack, and I followed the Pulsations but they just led me to the Celestial Dome s interface, But just to be safe keep an eye out Aelita Ok, I ll take you to the interface Aelita William Also Needs access to an Interface Alaya Wait. Which one needs more powerful interface? Aelita That would be me Alaya Odd, Yumi take William to the Tower Aelita Wait, Alaya what do you want me to do? Tony He can Come with us Ulrich Tony, Go with Ulrich and William Alaya Ok Tony

At the Celestial Dome s interface So what are you doing? Aelita Asks I am Reprogramming the Materialization programs Alaya What Aelita says in an Alert tone These programs must be altered to accommodate a transporter. After Which We should be Able to Transfer someone to and from this world Alaya What, you came here with out the ability to Go Back! Aelita I am not here Alaya Yes you are! Aelita I am on the USS Flux, inside Holodeck 1. I have programmed the computer to display this image of me because I feel that it is more efficient in this case to work Hands on This is the same with William and Tony Alaya explains Then how will you materialize us? At this point I can not, but I can have the computer do the reverse and project you as holograms, then I will apply the mobile emitters and you will assist me in my lab. What s a mobile emitter? Aelita asks because she thinks it won t make her sound dumb A Mobile emitter is a device that can project a hologram without the need for a Holodeck, or holographic emitters Oh Cool Aelita In the Tower in Carthage So your name is William Yumi Yes William What s with the Eyes? Odd Blurts out Odd! Yumi scolds him What are you an Alien Odd. Yumi punches Odd I am a member of the Groundskeepers William So you re a gardener? Odd No, My species prefers Groundskeepers to 8472 But you look so human Yumi My species can modify there appearance, I chose to Look human So what do you really look like? Odd asks 3 meters tall, tripedal, 5 sexes, powerful immune system, completely telepathic, biologically unique, and xenophobic William 5 Sexes!! Odd Yes. I am the 4th, Male William How did our people meet yours? Yumi During our war with the Borg William Who won? Odd Asks Humans assisted the Borg, as a result the Borg won Why are you serving on a crew with humans then? Yumi Humans sided with the Borg, because My people would have exterminated all life in the Galaxy William says camly Why!? Yumi and Odd ask startled Back then we believed ourselves to be perfect, and when the Borg invaded fluidic space we saw it as a threat to that perfection, our philosophy was The weak... will perish. William explains Who are the Borg? Alaya said those things on her hands were Borg. And your people went to war with them The Borg Collective is a Hive mind, people believed to have originated in the Delta quadrant. They are Single handedly responsible for the Destruction trillions of Individuals William Why would the do that kind of thing? Odd Because they seek to bring all Species from chaos into order . They seek one thing alone, Perfection William What s a Hive mind? You said the Borg were a hive mind Yumi asks The Individuals the Borg destroyed were assimilated into the Collective. They are now Merely drones. The Borg Think and act as one. Alaya joined them? Odd asks No she did not. The Borg assimilated her and her family along with the rest of the crew of The Mercy. No one chooses the Borg. I have seen almost a thousand people destroy them selves then become Drones. William Why don t people fight back? Odd asks The Borg Have the Collective Knowledge of tens of thousands of species, and trillions of individuals. They have all the technology those species had before assimilation. They also adapt to any weapon. Once my people could of destroyed them during that war but with the human weapons we ran back home. The Borg then adapted the weapons to assimilate us William Some where in the Core zone with Ulrich, Will, and Tony So Tony, your really good with a sword Ulrich My parents made me pick it up Tony How old are you? William 21 Tony Hey where did you get those Cool Clothes? These are our avatars for Lyoko Ulrich So when do I get one When you get an avatar Ulrich Hey Is that Alaya girl seeing any one? William asks No, why? Tony Because she is Hot William You don t want to go there Tony warns Why not? William How old are you? Tony asks 15 William responds 14 Ulrich She s like 20 Tony So William So. Did you see how how she acts? Tony Yes what s with that? William She isn t what you might call human Tony So she s like a Martian? William She s more like Borg Tony So, dose that mean that you like her? William No what would give you that idea Tony first you blushed when you woke up with her standing over you Ulrich Second, you did what she wanted you too quickly William Trust me you don t want to make her mad Tony Why? William Once when she first came aboard we had a guest who got a little drunk, he grabbed her arm and demanded she danced with him, She warned him that he should let go, he didn t and she dislocated his shoulder and knocked him unconscious, and walked to her lab. The point is she is Strong, and mean Alaya After 45 minuets they all went back to the Arena Computer, Freeze Odd, Ulrich, William, Aelita and Yumi Alaya What!! Why? Aelita manages to says before she is frozen Computer Activate Program Updates for Odd, Ulrich, William, Aelita, and Yumi Alaya Beginning Procedure Computer What are you doing? Tony I am Correcting flaws in there programs and I am increasing there age by approximately 6 years Alaya explains Why? Tony Because there programs are incapable of existing as a hologram, with out these modifications Alaya Process Complete Computer Computer Reset Program Parameters Alaya The Room Fades into static and returns to normal, The Lyoko worriers then fade out, and return as older versions of themselves. Everyone is much taller, Aelita s hair is slightly different, odd s isn t as pointy and he s taller then Aelita now, Yumi has hardly changed, Ulrich looks much more mature, Will looks in some ways similar to Tony, Odd, Ulrich, and Will are noticeably more muscular.  
Computer, Restore Odd, Ulrich, William, Aelita, and Yumi to operating order Alaya The Lyoko worriers regain there ability to move then they all fall on the floor unconscious Computer Begin Holographic Materialization, restore the Holodeck to original conditions Alaya The Holodeck changes back to the hologrid, but the Lyoko worriers are not there.  
On Lyoko in the Arena the Lyoko worriers begin to Devirtualize In the holodeck they soon appear in there Earth clothes on still unconscious Alaya grabs the mobile emitters and places them on the team Alaya that was sort of harsh. Don t you think? Tony It may have been Harsh but it was efficient Alaya Computer revive the subjects My head Odd holds his head in pain as he gets up Aelita Ulrich You all look different Yumi gets up Odd your hair! What about my hair Odd says as he places his hand on top of his head My HAIR!!!! he screams realizing he s lost the point in his hair Aelita! Aelita you look different. You hair is longer, and you re taller So are you, you re taller then me Aelita And Odd you look hotter, I mean that you are more muscular We re all taller and older Ulrich Points out Alaya, were detecting strange energy pulses coming from Holodeck 1, what are you doing? her comm. badge Captain Yates, Captain Paris would you please see me in your ready room Alaya says to here comm. Badge Yes. Of course. Right away Torrie In the Captains Ready Room Capitan I request that these five Holograms be completely materialize back to human form Alaya what your asking is a very complex and nearly impossible task to accomplish. Torrie But it can be done, It has already been done, many times Alaya If you can accomplish this task without any problems, you will be allowed an attempt to materialize these these people, but I will not interfere with your duties as a science officer Axum As for these People, They will be granted the rites equal to any guest Torrie 


	5. Chapter 5

Chapter 5 Dream On

In Alaya s Lab 2300 hours (11pm)  
Alaya is in her alcove regenerating, the Lyoko Worriers are sleeping on pillows. All is calm but Alaya is having another nightmare 3 of 12 auxiliary processor of Trimatrix 09, Your Wishes are Irrelevant. You will be assimilated. Resistance is futile the Voice of the Borg Nooo Alaya s mom screams Alaya Run, Hide!!! Her Dad Screams Alaya is running thru the halls of a Star Ship, a Borg Drone Steps Out of a Door You are Week. You Are Irrelevant. You are nothing with out the Collective but this time someone runs up and Stabs the Drone with a sharp piece of metal Alaya what s happening? The person asks scared Tony! Alaya hugs him Alaya What the Hell is going on! Tony Demands Alaya pushes him away and runs Alaya! Tony yells as he runs after her Get away from me. You re not real!! Alaya yells Alaya it s me Tony! What s going on?!? Tony yells as he gains on Alaya Get away!! Alaya Screams Alaya Calm Down Tony yells as he grabs her This isn t real, I m regenerating, and I m in my Alcove Alaya says Alaya I m Real, I don t know how but I m in your dream Tony Alaya opens her eyes How Do I know that your real You said this is a Dream, What if I do this Tony says as he Moves in to kiss her. Just before he dose Alaya grabs his face and knocks him onto the floor How would that have proved anything Alaya Demands Because Well I was hoping I was dreaming Unfortunately I can comprehend why you would want that Alaya says as Tony gets up. Alaya Grabs Tony s face and Kisses him on the lips for about 15 seconds then they both wake up In Tony s Room Tony wakes up and sit s up rubbing his head Dose that Count as A first Kiss? is all he says before he falls back to sleep In Alaya s lab Warning Regeneration cycle incomplete Computer Alaya screams a Girly scream, and runs to the replicator Breath Mint Alaya Demands. A Breath mint appears and Alaya takes it Alaya what s wrong Aelita Asks Just a bad dream Alaya stutters as she says it What about? Aelita Asks My parents Alaya I Know what that s like Aelita I do not want to talk about it Alaya, they don t notice but one of the panels goes black and a red Eye (The Eye of XANA) appears on it I find that talking Helps Aelita says before she starts Fizzing in and out Alaya Help Me!!! Aelita your program is being deleted Stop it Alaya thinking quickly uses her assimilation tubules and injects Nanoprobes into the Emitter Aelita you should be fine for now Alaya says reassuringly, Still unnoticed the panel goes back to normal What happened? Aelita I do not know, but it won t happen again, don t worry Alaya I need your help with modifying the Materialization programs Well I personally did not construct any Materialization programs but my father did, and I helped Jeremie program Code: Earth Aelita Who is Jeremie Alaya Jeremie was my dearest friend, he s the one who found me in the supercomputer. He also freed me from Lyoko. Aelita Aelita you re up? Will asks William Go back to sleep Aelita says soothingly Alaya, when do you think we ll get used to these older bodies? Will My estimate is 2 days Alaya Well I m having a strange felling in my lower body Will It may be because your Body is having trouble adapting to your holomatrix Well could you do something about it? Please Will Asks I am not an expert in holographic technology Alaya Do you know anyone who is? Will Ensign Jenkins Alaya Tony? Will Yes Alaya says as she holds her hand to her head Alaya are you hurting? Aelita No. I am fine Alaya says as her headache gets worse, and she stars to hear Talk about perfection Alaya also feels strange feelings that are defiantly not hers Tony? Alaya whispers as she collapses onto the floor unconscious.  
You guys!!! Help me get her to Sickbay Aelita yells. Aelita grabs Alaya s comm. badge Sickbay Alaya s hurt. Were taking her to you Everyone grabs Alaya and Carry her to sickbay. William already has a bed waiting What happened? Justin Gasman She was telling Will to ask Tony about a strange feeling in his legs and to talk to Tony, then she held her head like she was in pain then she fell onto the floor Aelita Explains Just then tony still in his night clothes (Boxers, and T-shirt) holding his head in pain Doctor I have a bad headache and Tony falls on the floor unconscious Tony! Justin says as he tries to wake Tony up Get him to the bed William instructs as Justin lays Tony on the bed Doctor what is going on? Aelita I don t know William Please Inform the Captain of Alaya and Tony s situation

In Alaya s Mind Moving thru a strange corridor, dark, and sparking lights, A Borg Vessel. Alaya is Regenerating In an Alcove, she is completely Borg. She wakes up, and begins to walk to an interface. At that point Tony runs past her, Alaya puts out her arm, he hits it and falls to the floor Who are you? Wait! Alaya! What is going on? Ton says Terrified We are 3 of 12 auxiliary processor of Trimatrix 09 Borg Alaya States, Alaya looks over at Tony, and in her normal voice says Tony? Tony Blinks and Alaya is in her normal clothes What is going on We are the Borg. You Will be assimilated. Says the Collective Tony we need to get out of here Alaya says as she pulls him up I agree Tony says as they run. Just as they turn the corner, There on another Ship Alaya, You re Messed up, why do you dream this stuff? he says as he turns to look at Alaya, but she is not there.  
Tony! Get out of my head Alaya yells form around the corner Wait? I don t even know how I got in!!! Tony yells as he follows her, on this next turn their in the void of space.

1 hour later on the Flux It appears that the left frontal lobe is being transformed into an interlink node, Tony, and Alaya are In effect connected into some form of Collective unconsciousness with each other. William tells Axum, and Torrie I do not know much about the Standard Interlink node but is it not impossible to remove the node without damaging him. Torrie Normally But This Node is imperfect, and only connects Tony to Alaya William Why did the nanoprobes only attempt to build an Interlink Node? Axum Because they had an insufficient supply of energy, and hoped to connect to the Collective and be reinforced William Explains Why were the Nanoprobes online in the first place? Axum After I reprogrammed all of them, I felt no harm in leaving them online. William Is there any chance that the Node could contact the Collective? Axum There is no threat William Ok. I give you the authority to remove the node Torrie

After the Operation.  
Alaya and, Tony have regained consciousness, but still feel each others thoughts.  
Get her out of My Head!! Tony pleads with the doctor Doctor, It is distracting. His thoughts are very distracting Alaya My thoughts?! Your thoughts are all so boring! Tony For the next few minuets Alaya and Tony argue, but William quickly sends them to work 


	6. Chapter 6

Chapter 6 I am attempting to make contact with you

We are about to exit the galaxy, proceeding to your duty stations Axum Announces Alaya runs to the turbo lift, just before the door closes Tony runs in Bridge Tony A few moments later Tony any feelings you may have felt, are completely Irrelevant, they were caused by extreme circumstances Alaya I understand Tony says in an unusual emotionless tone The turbo lift stops, and opens. Tony and Alaya take there Stations. Tony at Navigation, Alaya right behind hind him Prepare to Exit the Slip Stream Axum The ship goes to blue alert and begins to shake for a second Remodulate the shields to Alpha 6 configuration Torrie Done Rori Activate Transwarp Drive, and Exit the Barrier Axum The ship enters Transwarp, and bursts thru the Barrier, as it dose the Ship Shakes then returns to normal.  
How long to Star base 1116? Axum 4 hours 15 minuets Tony Captain Yates, I believe someone is attempting to merge into our Transwarp conduit. Alaya Allow them in Miss Rhodes Axum They have identified themselves as a federation star ship, the Kir Shara. The Kir Shara merges into the Conduit and, hails Hello, Flux Says the captain of the Kir Shara We are on our way to the Starbase 1116, we would love some company Well what a coincidence, so are we Axum Says in a oddly friendly tone Nice to see you again, Axis Says the other captain Captain, do you know him? Yes, me and Tak served aboard the Enterprise together, and I always messed up the aliment with the galactic axis, so they started calling me Axis Axum

In Alaya s Lab a while later So its Been 940 years since we last were on Lyoko Odd Asks Confused 939 years Alaya But it fells just like it was yesterday? William You are aware of the ageing process on Lyoko? Alaya Yes Aelita The Supercomputer was deactivated 939 years ago, and as a result you were rendered in to a state similar to Aelita when you first discovered her. As A Result you did not age until I advanced your programs. Alaya How long until you have the Materialization programs online? Yumi Asks I have almost completed the Virtualization and Materialization programs, but I an unable to finish without using more computer resources, I will have them finished once we arrive at Starbase 1116 Alaya explains Unnoticed behind the group, an Eye flashes on the screen and begins to transfer data to various stations around the ship On the bridge Captain Yates, Someone is tying to gain unauthorized access to the ships subspace transponder array. That someone is in Alaya s Lab Rori Informs Axum Stop Them! Torrie demands worrying about last time Alaya accessed the transponder Flash back to 4 months ago The flux is at red alert and all the Access terminals are a strange mix of Borg alphanumeric code and tcars formatting 3 of 12! Release control of the Transponder array Axum Shouts and he nods to Rori who has a disrupter rifle on her hand along with 3 other people in yellow (Security)  
Caption it has adapted to our weapons and has sealed it s self inside engineering! Some one says franticly over the intercom Over the intercom the voice of the Borg is heard A Borg proximity signal has been detected. Origin Unimatrix 114, Grid 19. Alter Corse to intercept The voice fades off (Present)  
Torrie, Contact Alaya and Ask what she s doing Axum In Alaya s Lab More Terminals have begun to display the Eye, Aelita Turns around and Yells XANA Alaya turns What? Zana? she asks confused, she then sees the eyes Aelita Tell me what is going on XANA s accessing your systems, Alaya there s no time to explain but you have to bock him you can Multitask, assist me and Explain Xana . Now Alaya Demands as she quickly starts pressing things into the interface Computer Encode program Alaya 2363-7782 Alaya demands the computer Complete Computer On the bridge Alaya! What is Going on down there Axum Yelled I don t know The computer cuts here off.  
Now the terminals on the bridge are starting to display the Eye Torrie What the hell is going on here?! Axum shouts I have no Idea Torrie At this time the intercom comes on Message directed towards Earth, Establish link with subspace relay station the computer voice says with a computerized almost demonic voice underlying it.  
Captian What ever it is, it s taking a copy of our technological and scientific database and leaving the ship Rori Track it! Axum The lights fade out and return to normal, the ship is fine In the Astrometrics Lab, Aelita and the gang, and Alaya, and the Senor staff are discussing XANA XANA is a multi agent program, He s smart, cunning, and evil. XANA is bent on enslaving humanity, and activates towers on Lyoko, and builds Replikas around the network. Or he did Aelita What happened to XANA William Jeremie built another multi agent system, and it destroyed all traces of XANA from the world, or so we thought Aelita says with a tear in her eye Aelita s father sacrificed himself to destroy XANA Odd informs them as Aelita rests her head on his shoulder And why would this XANA want our technological and scientific database? Axum It will help him improve him self, XANA is probably as confused as we are, and will be able to use that information to update himself and his knowledge of the world Aelita Xana also managed to copy most of the data for the memory cores before he left Which means that he can begin to build replikas William M How can a program affect so much of the real world Axum XANA activates towers on Lyoko to gain access to the real world Aelita is the only one capable of stopping the attack by deactivating the towers XANA Uses to attack the real world Ulrich Explains XANA is capable of possessing objects, programs, and people Will D Alaya, Can you track XANA? Axum Yes, but only the initial message, after that XANA will have the ability to infect the subspace relay stations without being detected Alaya Alaya presses a few things and a program starts up and displays an image of Lyoko, after much explanation they all head up to the bridge.  
Captains we are within range of the Starbase The Comm. officer informs Axum and Torrie On screen Torrie Captain Are you ok? We detected a massive power surge coming from your vessel, are you damaged The Station Administrator No we just had a bit of computer trouble We have a docking port ready for You and the Kir Shara The Station Administrator I must say, I am extremely excited to begin this experiment, Materialization of Virtual life forms, simply amazing We

Alaya is in her lab getting ready to transfer the Materialization programs to a Data Core Alaya beings to hear whispers she looks around but no one is there, the room goes quiet again. Alaya thinks nothing of it until it starts again and then she recognizes it, she hears it whenever there s Borg activity around, she s hearing the Collective Alaya still thinks nothing of it but she thinks she hears a voice specifically say 3 of 12" her Borg desigantion, which makes her a little nervous, but she tries to let it go. When she finishes she goes to the docking port, and together with Aelita, Odd, Ulrich, Will, and Yumi she goes to the Starbases transporter.  
Just before she begins the process, Alaya sends the holographic projections back to Lyoko, and activates the materialization program Materialization Aelita Alaya says as the transporter begins to reassemble Aelita In the real world after 10 seconds the process completes Alaya, I think that it worked, but I feel dizzy, I think I need to sit down Aelita says as she stumbles off the transporter pad Materialization Ulrich, Materialization Odd Alaya says, and this time the transporter begins to reassembles two bodies Alaya, Where are you from? Aelita asks out of nowhere What do you mean? Alaya Where were you born, where did you grow up? Aelita At this time Odd and Ulrich are materialized, and stumble down to where Aelita is sitting I was born on the Colony Angkor c, a research colony, I grew up there and I was assimilated near there Alaya Materialization Will, Materialization Yumi Again the process begins What was it like? Angkor c Aelita Asks as Will and Yumi materialize and go to sit down next to the rest of the gang Alaya pull up a seat Odd says as he pats the floor next to him It was an inhospitable world, Extreme Storms, wild Temperature Fluctuations, Active Geological systems Alaya responds Pull up a seat? Alaya asks confused Come sit with us Odd Explains I am unaccustomed to sitting, much less on the floor Alaya Come on Odd says as he stands up and pulls Alaya down to sit next to him Now tell us about yourself Will There is not much to tell Alaya Tell us about your life, your family, friends, and stuff like that Aelita I do not feel the relevance of informing you of my previous life. 


End file.
